Detecting modification of biomedical events using a deep parsing approach

Competing interests

The authors declare that they have no competing interests.

Authors' contributions

AM implemented the Task 3 system, including parsing of sentences and feature engineering. DM handled the various Task 1 systems, and implemented the NICTA system for Task 1. TB co-ordinated the study and participated in its design. All authors read, contributed to and approved the final manuscript.

Abstract

Background

This work describes a system for identifying event mentions in bio-molecular research abstracts that are either speculative (e.g. analysisof IkappaBalpha phosphorylation, where it is not specified whether phosphorylation did or did not occur) or negated (e.g. inhibitionof IkappaBalpha phosphorylation, where phosphorylation did not occur). The data comes from a standard dataset created for the BioNLP 2009 Shared Task. The system uses a machine-learning approach, where the features used for classification are a combination of shallow features derived from the words of the sentences and more complex features based on the semantic outputs produced by a deep parser.

Method

To detect event modification, we use a Maximum Entropy learner with features extracted from the data relative to the trigger words of the events. The shallow features are bag-of-words features based on a small sliding context window of 3-4 tokens on either side of the trigger word. The deep parser features are derived from parses produced by the English Resource Grammar and the RASP parser. The outputs of these parsers are converted into the Minimal Recursion Semantics formalism, and from this, we extract features motivated by linguistics and the data itself. All of these features are combined to create training or test data for the machine learning algorithm.

Results

Over the test data, our methods produce approximately a 4% absolute increase in F-score for detection of event modification compared to a baseline based only on the shallow bag-of-words features.

Conclusions

Our results indicate that grammar-based techniques can enhance the accuracy of methods for detecting event modification.

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